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Single-cell transcriptome analysis reveals effector CD8+ T cells may play an important role in residual chronic immune activation and inflammation in HIV-1 infected patients

ABSTRACT: Despite antiretroviral therapy (ART) suppressed viremia and reduced mortality in HIV-1 infected patients, residual chronic immune activation and inflammation in these patients can lead to an increased risk of non-communicable diseases, while the mechanism is still not clear. Harnessing scRNA-seq of PBMC of HIV-1 patients receiving ART and public avaialable scRNA-seq data, we found that the proportion of CD4+ T cells, CD8+ T cells, monocytes, and B cells showed variation in these patients. Through cluster analysis, it was found that effector CD8+ T cells were significantly decreased in HIV infected patients and lsATR, but increased in fsART, migration inhibitory factor (MIF) signaling was significantly increased in fsART.

ORGANISM(S): Homo sapiens

PROVIDER: GSE254301 | GEO | 2024/01/31

REPOSITORIES: GEO

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Project description:High levels of HIV-1 replication during the chronic phase of infection are usually associated with rapid disease progression (RP). However, a minority of HIV-infected individuals remain asymptomatic and show persistently high CD4+ T cell counts despite high viremia for many years (viremic non progressors, VNP). The latter profile is reminiscent of the non-pathogenic model of SIV infection in natural hosts such as the sooty mangabey. We used various genomic approaches to examine 66 RP and 6 VNP defined according to strict criteria. RP were characterized by depletion of protective HLA alleles, enrichment of HLA alleles associated with disease progression, and a characteristic transcriptome profile of CD4+ and CD8+ T cells similar to that observed in pathogenic SIV infection of rhesus macaque. In contrast, VNPs presented lower expression of interferon stimulated genes than RP, and shared with SIV-infected sooty mangabeys a common profile of regulation of a set of genes that includes CASP1, CD38, LAG3, TNFSF13B, SOCS1 and EEF1D. The estimated 8% of RP and 0.1% of VNP in human cohorts represent two subsets of HIV-infected individuals whose analysis may inform our understanding of HIV pathogenesis. Selection criteria rapid progressors (RP): HIV seroconversion window <1 year WITH documented negative and positive serology or biological proof of primary infection. AND One of A) or B) A) >2 CD4+ T cell counts below 350 cells/µl within 3 years of seroconversion AND no subsequent rise of CD4+ T cells above 350 cells/µl in the absence of ART. B) ART initiated within 3 years of seroconversion AND CD4+ T cell count within 1 month of ART-start <350 cells/µl. Selection criteria viremic non progressors (VNP): > 3 years of follow-up AND median HIV viremia from >3 measurements >100'000 viral RNA copies/ml AND HIV viremia consistently above 10’000 copies/ml AND CD4+ T cell count above 350 cells/µl AND no ART during follow-up. Selection criteria elite/viremic controllers (EC): see Casado et al. 2010. Host and viral genetic correlates of clinical definitions of HIV-1 disease progression. PLoS ONE 5:e11079. Total RNA from 41 samples obtained from CD4 T cells from HIV infected individuals to identify associations between gene expression and different distinct patterns of disease progression Total RNA from 38 samples obtained from CD8 T cells from HIV infected individuals to identify associations between gene expression and different distinct

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Single-cell transcriptome analysis reveals effector CD8+ T cells may play an important role in residual chronic immune activation and inflammation in HIV-1 infected patients

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